Sure, the sun is pretty important, what with the whole sun-flare-killing-oodles-of-people thing. But what about the good ol' sky?
For Mark, the sky symbolizes something a little more than just "that blue or gray or black thing up there." When he was young, his mother used to teach him about the constellations, and he would pass on the stories to his little sister, Madison:
He spotted Orion, the belt brighter than he'd ever seen it before. Orion. That had been Madison's favorite constellation because it was so easy to find and had such a cool story behind it—the hunter and his sword, his dogs, all of them fighting a demonic bull. (15.25)
This symbol goes along with the whole "Memory and the Past" theme (check out our "Themes" section for more informational goodness on that). For Mark, the sky reminds him of constellations, which in turn reminds him of Madison, which then gives him a sinking feeling. Because, you know, he's pretty sure Madison is dead.
So yeah, the sky isn't a very fun symbol, since it's a reminder of two things for Mark: the sun-flares and his (most likely) dead sister.
But there's also another layer behind the sky's symbolism. Notice how Mark mentions the "cool story behind" Orion? This should remind you of another "cool story" behind a story—The Kill Order. The Kill Order functions as the story behind the Maze and the Maze Runner trilogy. Orion's fighting of the demonic bull can be seen as running parallel to Mark's fighting demonic hoards of insane humans—he can only hope that, one day, people will remember his story with the same fondness they remember the saga of Orion.